Optimal sum-of-pairs multiple sequence alignment using incremental Carrillo and Lipman bounds
Author
Konagurthu, AS; Stuckey, PJDate
2006-04-01Source Title
JOURNAL OF COMPUTATIONAL BIOLOGYPublisher
MARY ANN LIEBERT, INCAffiliation
Computer Science and Software EngineeringMetadata
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Journal ArticleCitations
Konagurthu, A. S. & Stuckey, P. J. (2006). Optimal sum-of-pairs multiple sequence alignment using incremental Carrillo and Lipman bounds. JOURNAL OF COMPUTATIONAL BIOLOGY, 13 (3), pp.668-685. https://doi.org/10.1089/cmb.2006.13.668.Access Status
This item is currently not available from this repositoryAbstract
Alignment of sequences is an important routine in various areas of science, notably molecular biology. Multiple sequence alignment is a computationally hard optimization problem which involves the consideration of different possible alignments in order to find an optimal one, given a measure of goodness of alignments. Dynamic programming algorithms are generally well suited for the search of optimal alignments, but are constrained by unwieldy space requirements for large numbers of sequences. Carrillo and Lipman devised a method that helps to reduce the search space for an optimal alignment under a sum-of-pairs measure using bounds on the scores of its pairwise projections. In this paper, we generalize Carrillo and Lipman bounds and demonstrate a novel approach for finding optimal sum-of-pairs multiple alignments that allows incremental pruning of the optimal alignment search space. This approach can result in a drastic pruning of the final search space polytope (where we search for the optimal alignment) when compared to Carrillo and Lipman's approach and hence allows many runs that are not feasible with the original method.
Keywords
Artificial Intelligence and Image ProcessingExport Reference in RIS Format
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